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Class: QualityMetrics

Quality metrics for experiments

URI: lambdaber:QualityMetrics

classDiagram class QualityMetrics click QualityMetrics href "../QualityMetrics/" AttributeGroup <|-- QualityMetrics click AttributeGroup href "../AttributeGroup/" QualityMetrics : anom_corr QualityMetrics : anom_sig_ano QualityMetrics : anomalous_used QualityMetrics : average_b_factor_a2 QualityMetrics : cc_half QualityMetrics : clashscore QualityMetrics : completeness QualityMetrics : completeness_high_res_shell_percent QualityMetrics : description QualityMetrics : i_zero QualityMetrics : mean_i_over_sigma_i QualityMetrics : molprobity_score QualityMetrics : multiplicity QualityMetrics : r_factor QualityMetrics : r_free QualityMetrics : r_merge QualityMetrics : r_pim QualityMetrics : r_work QualityMetrics : ramachandran_favored_percent QualityMetrics : ramachandran_outliers_percent QualityMetrics : resolution QualityMetrics : resolution_high_shell_a QualityMetrics : resolution_low_a QualityMetrics : rg QualityMetrics : signal_to_noise QualityMetrics : space_group QualityMetrics : unit_cell_a QualityMetrics : unit_cell_alpha QualityMetrics : unit_cell_b QualityMetrics : unit_cell_beta QualityMetrics : unit_cell_c QualityMetrics : unit_cell_gamma QualityMetrics : wilson_b_factor_a2

Inheritance

Slots

Name Cardinality and Range Description Inheritance
resolution 0..1
Float		 Resolution in Angstroms direct
resolution_high_shell_a 0..1
Float		 High resolution shell limit in Angstroms direct
resolution_low_a 0..1
Float		 Low resolution limit in Angstroms direct
completeness 0..1
Float		 Data completeness percentage direct
completeness_high_res_shell_percent 0..1
Float		 Completeness in highest resolution shell direct
signal_to_noise 0..1
Float		 Signal to noise ratio direct
mean_i_over_sigma_i 0..1
Float		 Mean I/sigma(I) direct
space_group 0..1
String		 Crystallographic space group direct
unit_cell_a 0..1
Float		 Unit cell parameter a in Angstroms direct
unit_cell_b 0..1
Float		 Unit cell parameter b in Angstroms direct
unit_cell_c 0..1
Float		 Unit cell parameter c in Angstroms direct
unit_cell_alpha 0..1
Float		 Unit cell angle alpha in degrees direct
unit_cell_beta 0..1
Float		 Unit cell angle beta in degrees direct
unit_cell_gamma 0..1
Float		 Unit cell angle gamma in degrees direct
multiplicity 0..1
Float		 Data multiplicity (redundancy) direct
cc_half 0..1
Float		 Half-set correlation coefficient CC(1/2) direct
r_merge 0..1
Float		 Rmerge - merge R-factor direct
r_pim 0..1
Float		 Rpim - precision-indicating merging R-factor direct
wilson_b_factor_a2 0..1
Float		 Wilson B-factor in Angstroms squared direct
anomalous_used 0..1
Boolean		 Whether anomalous signal was used direct
anom_corr 0..1
Float		 Anomalous correlation direct
anom_sig_ano 0..1
Float		 Anomalous signal strength direct
r_work 0..1
Float		 Refinement R-factor (working set) direct
r_free 0..1
Float		 R-free (test set) direct
ramachandran_favored_percent 0..1
Float		 Percentage of residues in favored Ramachandran regions direct
ramachandran_outliers_percent 0..1
Float		 Percentage of Ramachandran outliers direct
clashscore 0..1
Float		 MolProbity clashscore direct
molprobity_score 0..1
Float		 Overall MolProbity score direct
average_b_factor_a2 0..1
Float		 Average B-factor in Angstroms squared direct
i_zero 0..1
Float		 Forward scattering intensity I(0) direct
rg 0..1
Float		 Radius of gyration in Angstroms direct
r_factor 0..1
Float		 R-factor for crystallography (deprecated, use r_work) direct
description 0..1
String		 AttributeGroup

Usages

used by used in type used
ExperimentRun quality_metrics range QualityMetrics

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type Mapped Value
self lambdaber:QualityMetrics
native lambdaber:QualityMetrics

LinkML Source

Direct

name: QualityMetrics
description: Quality metrics for experiments
from_schema: https://w3id.org/lambda-ber-schema/
is_a: AttributeGroup
attributes:
  resolution:
    name: resolution
    description: Resolution in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  resolution_high_shell_a:
    name: resolution_high_shell_a
    description: High resolution shell limit in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  resolution_low_a:
    name: resolution_low_a
    description: Low resolution limit in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  completeness:
    name: completeness
    description: Data completeness percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  completeness_high_res_shell_percent:
    name: completeness_high_res_shell_percent
    description: Completeness in highest resolution shell
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  signal_to_noise:
    name: signal_to_noise
    description: Signal to noise ratio
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  mean_i_over_sigma_i:
    name: mean_i_over_sigma_i
    description: Mean I/sigma(I)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  space_group:
    name: space_group
    description: Crystallographic space group
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
  unit_cell_a:
    name: unit_cell_a
    description: Unit cell parameter a in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_b:
    name: unit_cell_b
    description: Unit cell parameter b in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_c:
    name: unit_cell_c
    description: Unit cell parameter c in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_alpha:
    name: unit_cell_alpha
    description: Unit cell angle alpha in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_beta:
    name: unit_cell_beta
    description: Unit cell angle beta in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_gamma:
    name: unit_cell_gamma
    description: Unit cell angle gamma in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  multiplicity:
    name: multiplicity
    description: Data multiplicity (redundancy)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  cc_half:
    name: cc_half
    description: Half-set correlation coefficient CC(1/2)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  r_merge:
    name: r_merge
    description: Rmerge - merge R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  r_pim:
    name: r_pim
    description: Rpim - precision-indicating merging R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  wilson_b_factor_a2:
    name: wilson_b_factor_a2
    description: Wilson B-factor in Angstroms squared
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  anomalous_used:
    name: anomalous_used
    description: Whether anomalous signal was used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: boolean
  anom_corr:
    name: anom_corr
    description: Anomalous correlation
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  anom_sig_ano:
    name: anom_sig_ano
    description: Anomalous signal strength
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  r_work:
    name: r_work
    description: Refinement R-factor (working set)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  r_free:
    name: r_free
    description: R-free (test set)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  ramachandran_favored_percent:
    name: ramachandran_favored_percent
    description: Percentage of residues in favored Ramachandran regions
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  ramachandran_outliers_percent:
    name: ramachandran_outliers_percent
    description: Percentage of Ramachandran outliers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  clashscore:
    name: clashscore
    description: MolProbity clashscore
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  molprobity_score:
    name: molprobity_score
    description: Overall MolProbity score
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  average_b_factor_a2:
    name: average_b_factor_a2
    description: Average B-factor in Angstroms squared
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  i_zero:
    name: i_zero
    description: Forward scattering intensity I(0)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  rg:
    name: rg
    description: Radius of gyration in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float
  r_factor:
    name: r_factor
    description: R-factor for crystallography (deprecated, use r_work)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - QualityMetrics
    range: float

Induced

name: QualityMetrics
description: Quality metrics for experiments
from_schema: https://w3id.org/lambda-ber-schema/
is_a: AttributeGroup
attributes:
  resolution:
    name: resolution
    description: Resolution in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: resolution
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  resolution_high_shell_a:
    name: resolution_high_shell_a
    description: High resolution shell limit in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: resolution_high_shell_a
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  resolution_low_a:
    name: resolution_low_a
    description: Low resolution limit in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: resolution_low_a
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  completeness:
    name: completeness
    description: Data completeness percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: completeness
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  completeness_high_res_shell_percent:
    name: completeness_high_res_shell_percent
    description: Completeness in highest resolution shell
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: completeness_high_res_shell_percent
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  signal_to_noise:
    name: signal_to_noise
    description: Signal to noise ratio
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: signal_to_noise
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  mean_i_over_sigma_i:
    name: mean_i_over_sigma_i
    description: Mean I/sigma(I)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: mean_i_over_sigma_i
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  space_group:
    name: space_group
    description: Crystallographic space group
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: space_group
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: string
  unit_cell_a:
    name: unit_cell_a
    description: Unit cell parameter a in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: unit_cell_a
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_b:
    name: unit_cell_b
    description: Unit cell parameter b in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: unit_cell_b
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_c:
    name: unit_cell_c
    description: Unit cell parameter c in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: unit_cell_c
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_alpha:
    name: unit_cell_alpha
    description: Unit cell angle alpha in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: unit_cell_alpha
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_beta:
    name: unit_cell_beta
    description: Unit cell angle beta in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: unit_cell_beta
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  unit_cell_gamma:
    name: unit_cell_gamma
    description: Unit cell angle gamma in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: unit_cell_gamma
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  multiplicity:
    name: multiplicity
    description: Data multiplicity (redundancy)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: multiplicity
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  cc_half:
    name: cc_half
    description: Half-set correlation coefficient CC(1/2)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: cc_half
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  r_merge:
    name: r_merge
    description: Rmerge - merge R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: r_merge
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  r_pim:
    name: r_pim
    description: Rpim - precision-indicating merging R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: r_pim
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  wilson_b_factor_a2:
    name: wilson_b_factor_a2
    description: Wilson B-factor in Angstroms squared
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: wilson_b_factor_a2
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  anomalous_used:
    name: anomalous_used
    description: Whether anomalous signal was used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: anomalous_used
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: boolean
  anom_corr:
    name: anom_corr
    description: Anomalous correlation
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: anom_corr
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  anom_sig_ano:
    name: anom_sig_ano
    description: Anomalous signal strength
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: anom_sig_ano
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  r_work:
    name: r_work
    description: Refinement R-factor (working set)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: r_work
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  r_free:
    name: r_free
    description: R-free (test set)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: r_free
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  ramachandran_favored_percent:
    name: ramachandran_favored_percent
    description: Percentage of residues in favored Ramachandran regions
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ramachandran_favored_percent
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  ramachandran_outliers_percent:
    name: ramachandran_outliers_percent
    description: Percentage of Ramachandran outliers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ramachandran_outliers_percent
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  clashscore:
    name: clashscore
    description: MolProbity clashscore
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: clashscore
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  molprobity_score:
    name: molprobity_score
    description: Overall MolProbity score
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: molprobity_score
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  average_b_factor_a2:
    name: average_b_factor_a2
    description: Average B-factor in Angstroms squared
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: average_b_factor_a2
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  i_zero:
    name: i_zero
    description: Forward scattering intensity I(0)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: i_zero
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  rg:
    name: rg
    description: Radius of gyration in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: rg
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  r_factor:
    name: r_factor
    description: R-factor for crystallography (deprecated, use r_work)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: r_factor
    owner: QualityMetrics
    domain_of:
    - QualityMetrics
    range: float
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: description
    owner: QualityMetrics
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string